A Bad Storm
by Atarya QueenofEgypt
Summary: A severe thunderstorm hits Domino City and as Solomon Muto is out of the house for a few hours, it's just Yugi and Yami. As Yugi is spending time with his love, he begins to hear a rumble of thunder. Can Yami help his love Yugi? (Takes place after the ceremonial duel and Yami comes back to be with Yugi. Puzzleshipping and yaoi will be included.)
1. Sensing Danger

**Author's Note:**

 **Hey, guys. This will be my first ever Yu-Gi-Oh story that I am writing on my own. I hope that you all enjoy it and keep reading and reviewing. By the way, when Yami came back, he had a separate body.**

 **Disclaimer: I don't own Yu-Gi-Oh or its characters.**

It was a cloudy and warm day in Domino City. The sky was covered in gray clouds. It looked like it was going to do something.

The bell began to ring at Domino High and it was time for everyone to go home.

Yugi Muto and Yami Sennen were walking hand in hand over to where the lockers and across from the lockers was the doors that led out of the school.

Yugi sat down on a bench with Yami. The two boys were still holding hands.

Joey, Tristan and Tea came walking over to the two boys, seeing that one was taller than the other.

"Hey, Yuge. Hi, Pharaoh." Joey said as they were approaching Yugi and Yami.

Yami began to hear Joey's voice.

Yugi turned around and saw his friends approaching.

"Hey guys." Yugi said as they were now standing in front of him and Yami.

"Hey, little buddy. Glad to see you and the Pharaoh together." Tristan said, looking at Yugi as he was holding Yami's hand.

Yugi looked into Yami's purple eyes and Yami looked into his partner's eyes.

"Well, ever since Yami left, I have been crying myself to sleep every night, wishing for him to come back." Yugi said as Yami was embracing him in a hug.

"It's true. Even after the ceremonial duel, a new evil arrived and Isis opened a portal for me and I was reborn. My job isn't done yet. I still have to take care of my lover and rid the world of all evil." Yami said, explaining about why he came back.

Tea was silent.

Joey and Tristan looked at her.

"Tea, don't ya approve of Yugi and da Pharaoh being together? I support it." Joey said as he looked at the brown haired girl.

Tea's blue eyes looked at Yugi and Yami.

She didn't like gays. She was more of a straight person but, she knew that Yugi and Yami had more than a brother relationship.

Seeing the two together made her sick.

She looked at the watch that was on her wrist.

"Oh my. Look at the time. I'm late." Tea said, an awkward smile on her face.

"Late for what, Tea?" Yugi asked as he looked away from his partner to look at her.

Tea scoffed at him.

"Why should I tell you?" Tea said, in an angry voice.

"Tea, we're your friends." Yami said, reassuringly.

Tea looked at Yami and scoffed.

"Friends? You and Yugi friends to me?! Hmph." Tea said as she crossed her arms and was now walking towards the double glass doors.

She was hurt, jealous, angry and frustrated.

"Forget her, Yuge." Joey said, hoping that Yugi wouldn't be worried about his and Yami's relationship.

Yugi looked at Joey and nodded.

"So, little buddy, where are you and the Pharaoh headed to this afternoon?" Tristan asked as he was changing the subject so that they would forget about Tea's resentful ways.

Yugi looked at Yami.

"Well, Yami and I are going home. Grandpa said that he had to talk to us about something important." Yugi said, remembering what happened this morning during breakfast.

Yami looked at the double glass doors.

The sky was beginning to get darker and darker with storm clouds.

"We better be going home now. I'm sorry if we can't stick around for much longer." Yami said as he was helping Yugi stand up.

"Why do ya say that, Pharaoh?" Joey asked, wondering.

Then, the Eye of Udjat was beginning to appear on Yami's forehead.

Tristan and Joey took a step back.

"What da...What da hell is that?" Joey said as he leapt onto Tristan.

Tristan was now cradling Joey in his arms.

Joey was shaking and his teeth were chattering.

Yugi was laughing.

"Joey, it's okay. Yami has ancient powers. Right, Yami?" Yugi said, reassuringly as he was now looking from to his best friend to Yami.

"I'm sensing something, Yugi." Yami said as the Eye of Udjat was still glowing on his forehead.

"What is it, Yami?" Yugi said, wondering but concerned at the same time.

"I'm sensing a strong disturbance that's not far from here but, is moving at 12 miles per hour, getting closer and closer. " Yami said as the Eye of Udjat was now beginning to disappear.

Tristan shoved Joey off of him and Joey was now on the floor.

Joey got back up and growled at Tristan.

"Well, whatever it is, you two should get safely home." Tristan said as he looked from Yami and Yugi to Joey, who was growling at him.

Yami looked at Yugi.

"Ready to go home, Yugi?" Yami asked.

Yugi nodded his head yes, silently.

"See you two tomorrow at Duke's. How does two o'clock sound to the both of you?" Yami said as he was holding Yugi's hand and now was about to walk with Yugi towards the doors.

"Sounds good, Pharaoh." Joey said.

"Yep." Tristan said.

Yugi and Yami were now walking towards the double glass doors.

Joey and Tristan were watching as Yugi and Yami were just about to walk out the double glass doors.

Yugi and Yami waved goodbye to them.

Joey and Tristan waved goodbye as Yugi and Yami were now walking out the doors, heading out into the darkened stormy sky.

 **(Whoa. So, Tea has something against Yugi and Yami being together. Will she get over it or should she just accept the relationship that Yugi and Yami are in? Hope that you enjoyed chapter one and stay tuned for chapter two. Please read and review.)**


	2. The Flashback

As Yugi and Yami were walking together towards Domino Boulevard, where their home, known as the Kame Game Shop was located at, Yugi was beginning to wonder about what Grandpa had said this morning.

Yami kept his eyes on his lover as he was walking, holding onto Yugi's hand as Yugi was beginning to flashback to this morning.

 _~Flashback~_

 _It was a beautiful Friday morning._

 _The sun was shining and the birds were singing a happy tune, to greet the start of the glorious morning._

 _Friday was one of those days where Yugi liked to sleep in a little bit more before the alarm went off at 7:00 a.m._

 _The sun was shining through the lavender drapes and as Yugi was sleeping, he could hear several robins sing their happy tune._

 _Just then, the red numbers that were displaying on the digital alarm clock changed from 6:59 a.m. to 7:00 a.m._

 _The tune of the Hampsterdance by Hampton and the Hamsters began to play as the red digital numbers were now flashing._

 _Yugi began to awaken to the melodic and uplifting tune that was playing._

 _He was rubbing the sleep from his eyes and after he got fully woken up, he got up from where he was sleeping with Yami and walked over to where the nightstand was._

 _When he got over there, he pressed the snooze button and looked back over at Yami._

 _Yami was sleeping so peacefully, like a baby._

 _Yugi couldn't help but blush._

 _He didn't want to wake up his lover but, he knew that this weekend, they could sleep and cuddle for as long as they wanted to._

 _Yugi walked back over to where Yami was sleeping._

 _Just when Yugi got to him, he climbed onto the bed and was now crawling onto Yami._

 _He sat down on Yami's pelvis and leaned in._

 _His head landed on Yami's right shoulder._

 _He looked at Yami's eyes that were closed and had an idea._

 _Yugi began to lean over and began to kiss Yami's lips._

 _As Yami was sleeping, he could hear the 'chu' sound of Yugi kissing him._

 _Yami's purple eyes began to open and his lips began to make contact with Yugi's._

 _Yami stopped the kiss for a while and placed Yugi on his lap, cradling the small boy, like a baby._

" _Good morning, my love." Yami said as he looked into Yugi's purple eyes, romantically._

 _Yugi's cheeks were blushing red._

" _Good morning, Yami." Yugi said as he was sitting on Yami's lap, looking at him, smiling._

 _Yugi's eye gaze went from Yami's eyes all the way down towards the bigger boy's pelvis._

 _Yami followed the smaller boy's gaze._

" _Would my little boy like to ride me like a little horsey?" Yami said, in a babyish but rather sexy voice._

 _Yugi looked at the door._

 _Solomon Muto, Yugi and Yami's grandfather would be here any minute to tell the two boys that it's time for breakfast and to get ready for school._

" _You alright, Yugi?" Yami asked as he saw a worried expression on Yugi's face._

 _Yugi looked at the wooden door's outline and saw no shadow._

 _He sighed in relief._

 _Yugi then looked into Yami's purple eyes._

" _How about we make it a three minute ride and we can hold hands throughout the day?" Yugi said, making Yami an offer that he can't refuse._

" _You got yourself a deal." Yami said as he began to take off his pants and underwear._

 _After he did that, he laid back down onto the bed, with his ding-dong sticking out._

 _Yami loved being sexy with Yugi when the two were being together and not interrupted by the real world._

 _Yugi was a male on the outside but a female at heart._

 _Yami looked at Yugi as he was getting undressed out of his aquamarine pajama pants and his white underwear._

 _Yugi looked back at Yami._

 _Yami gave him a romantic look that said… 'show me the merchandise'._

 _Yugi smiled and blushed._

 _This was quite awkward for him but, he knew that his wish would be granted, making it a very good Friday._

 _Yugi was done taking off his pants and underwear but, something was missing._

 _Yami instantly knew what that missing thing was._

" _Yugi, can you hand me your gold sarcophagus and your duel disk?" Yami asked._

 _Yugi blushed and did what his Pharaoh told him to do._

 _Yami opened the gold sarcophagus that had the Egyptian hieroglyphics and the Eye of Udjat on it,in the front._

 _He took the cards out of it and looked through the deck, shuffling carefully until he found the blue Mystical Elf._

 _He then took it out of the deck and placed the other cards orderly and nicely back into the sarcophagus._

 _Yami gave the gold sarcophagus back to Yugi and Yugi placed it onto his desk._

 _He then looked at Yami._

" _Yami, why do you need my duel disk and the Mystical Elf?" Yugi asked, puzzled._

 _Yami chuckled._

" _My little sexy boy, you will see why." Yami said._

 _The Eye of Udjat was appearing on Yami's forehead._

 _Yugi looked down at the card that Yami was holding and was just about to activate it._

 _As the Eye of Udjat was glowing on Yami's forehead, the card was glowing and the Mystical Elf began to come out._

 _Just when she came out, Yami kept his focus on Yugi._

 _He could sense that Yugi was panicking so, he looked at the Mystical Elf, who was now glowing and beginning to chant._

 _He then looked back at Yugi as he held his hand out, in front of Yugi._

 _It was too late to call off the procedure._

 _The Mystical Elf was getting stronger and stronger by every passing second._

' _I'm so sorry, Yugi.' Yami said to himself as the Mystical Elf and him were now transforming Yugi with the magic, into a female._

 _Yugi's starfish hair was now long and purple and black. His body was skinny and, instead of having a ding-dong, he had a woman part._

 _Yami's magic and the Mystical Elf's magic had actually made Yugi into a transgender._

 _Yugi began to twirl around, showing his half naked glory._

" _Love, you look amazingly pretty." Yami said as he looked at his transgender lover._

" _Thanks, Yami." Yugi said, cheerful and giddy as he walked back over to Yami._

 _Yami reached out to Yugi and Yugi was now being held on Yami's pelvis._

 _Yami then got up off of the bed and laid Yugi down._

 _Yugi's peach was showing._

 _Yami now began to get back onto the bed, sitting down on Yugi's pelvis._

 _Yami's ding-dong was now ready to mate with Yugi's peach._

 _Yami then placed his ding-dong into Yugi's 'vagina'._

 _Yugi was blushing._

" _Like it, love?" Yami asked._

 _Yugi was sweating a little bit but, nodded his head yes._

 _Yami then rolled them both over and now, Yugi was on top._

 _This startled Yugi a little bit._

" _Yami, do we have to do this?" Yugi asked, a little unsure._

 _Yami was blushing too._

" _If you're feeling comfortable doing it with me and your clothes off." Yami said, feeling a little bit awkward._

 _Yugi looked into Yami's eyes, romantically._

" _I'm ready." Yugi said and then, he began to ride Yami, moving in and out with his peach, creating a rhythm that both of them could dance to._

 _Yami then began to dance along with Yugi, moving his ding-dong in and out._

 _Yami was really quite enjoying it._

 _He really liked Yugi being this way, romantic and sexy but, he was going to miss it when Yugi was back to being a male._

 _3 minutes later…_

 _Yami and Yugi were now sitting beside each other on the bed._

 _The spell had only lasted for that long and now, Yugi was back to being a male._

 _Yugi was red in the face._

" _Yugi, are you alright?" Yami asked, concerned._

 _He was afraid that he had done something wrong to the little boy._

 _Yugi then looked at Yami._

" _I feel...rather embarrassed." Yugi said, looking at Yami and blushing._

 _Yami then began to hug Yugi._

" _It's okay, little one. I still love you no matter what gender you are or choose to be." Yami said, comfortingly._

 _Yugi looked into Yami's eyes, romantically and Yami looked into Yugi's eyes the same way._

 _Yugi looked at the digital clock._

 _It was 7:10._

" _Well, little one, shall we get ready for school?" Yami asked as he looked at the digital clock with Yugi._

 _Yugi nodded his head yes._

 _Then, Yugi and Yami began to get ready for school._

 _Just as Yugi was putting on his pants, Yami came up from behind him and he placed both hands on the little boy's ass._

 _Yugi blushed and resumed putting on his school clothes._

 _After the two boys were done getting dressed, they could hear an old man's voice calling them downstairs for breakfast._

" _Ready, Yugi?" Yami asked as he looked at the boy and held his hand out._

 _Yugi now held his hand in Yami's._

" _Ready, Yami." Yugi said as he looked Yami, determinedly in his eyes._

 _Yami could feel Yugi's confidence pulling them closer and closer to the door._

 _Yami opened the door and Yugi began to walk out first._

 _He was glad that the awkward stuff that Yugi and him did was now all behind them, in their bedroom._

 _Yugi and Yami walked down the flight of stairs together and reached the living room area._

" _Grandpa?" Yugi said, worried._

 _They then waited a minute._

" _In here, Yugi." Solomon Muto's voice replied, from the dining room._

 _Yugi and Yami hurriedly ran into the dining room._

 _They saw Solomon Muto sitting down at the table, enjoying his cup of coffee and toast, with jelly._

" _Grandpa, you made this?" Yugi asked, quite surprised at his grandfather's cooking abilities._

" _Anything for my grandson and his boyfriend Pharaoh." Solomon Muto said as Yugi and Yami were now sitting down together, beside each other._

 _Yami then began to raise his orange juice glass._

" _I would like to make a toast." Yami said as he stood up, holding Yugi's hand._

" _And what if I were to decline?" Solomon Muto said._

 _Yugi was shocked._

" _Grandpa?!" Yugi said, worried._

 _Solomon was laughing._

" _Oh, Yugi. Don't be sad. I was only joking." Solomon Muto said, seeing that Yugi couldn't take a joke very seriously._

 _Yugi then sighed in relief and looked at Yami, with an interest in his eyes as he was now holding up his glass of orange juice._

 _Solomon then followed his grandson's gaze._

" _Grandpa…?" Yami said, quite awkwardly._

 _Yami remembered Yugi's grandfather as his counselor in Ancient Egypt, when he ruled as Pharaoh._

" _Yes, Yami?" Solomon Muto replied, looking at the Pharaoh._

" _Mind if I propose my toast Yugi so that we can eat and head to the building of education?" Yami asked._

" _Sure but, why are you in such a hurry?" Solomon said, hearing the hastiness in Yami's voice._

" _I...I don't want my little one to be late." Yami said as he was now looking at Yugi and winking._

 _Yugi smiled._

 _Solomon sighed._

" _Alright. Make it quick." Solomon said, giving in._

 _He could see that Yami loved Yugi and he knew that Yami wanted much more for the little boy._

 _Yami then looked at Yugi._

" _To a great day and for the love of my life." Yami said as he held his glass up and looked at Yugi, smiling._

" _The same thing goes for the love of my life, Yami Millennium Sennen." Yugi said as he was also holding his glass up and looking at Yami._

 _The two smiled and clinked their drinking glasses together._

 _After that, they began to eat breakfast._

 _Just after they got done eating breakfast, Yugi and Yami went into the living room to get their backpacks._

 _Yugi was bouncing up and down._

 _Yami held him in place._

" _Is my little boy ready to go to school?" Yami asked as he looked at Yugi._

" _Yes, Yami. I'm ready." Yugi said, eager and excited._

 _Yami chuckled and began to hold Yugi's hand._

 _Just as they were about to head out the door, Solomon Muto held his hand out, to stop the two._

" _Pharaoh! Yugi!" Solomon Muto said as the two boys were now about to walk out the door._

 _Yami looked at Yugi._

" _Wait outside for me, little one. Don't go roaming around." Yami said, in a parental and fatherly voice._

 _Yugi nodded and went outside._

 _Just after Yugi went outside and stood beside the sign, waiting for Yami, inside… Yami looked back at the old man._

" _Yes, Solomon?" Yami said, a little bit annoyed._

" _Between you and me, I have to go somewhere this afternoon, which, of course will break Yugi's heart but, I need you to watch Yugi for me. You're really good at protecting him from bullies." Solomon began to say, in an explanation._

 _Yami sighed and looked at his gold watch._

 _It was 7:25._

" _So, how did you know that I protect him from bullies? I couldn't save him from Rafael. He saved me." Yami asked, remembering when he lost Yugi to an Orichalcos duel but, got Yugi back after he defeated Dartz._

" _Joey told me. He said that you protected him from that clown fellow… What's his name?" Solomon said as he was beginning to think._

" _Panik." Yami said, remembering the name._

 _Yami did remember Panik._

 _Panik was a big bully and a strong duelist but, a coward at heart._

 _Though, he did open Panik's mind in the end._

 _Yami even wondered if Panik really changed after Duelist Kingdom._

 _Yami knew what he was going to do this afternoon._

 _He was going to call Panik and see how the guy was._

 _Yami then looked at the door._

" _I must be heading out. Yugi might have a conniption fit if I have been keeping him waiting for so long." Yami said as he looked at the door._

 _Solomon nodded his head in agreement._

" _Take good care of him, Pharaoh." Solomon said as Yami was opening the door and now about to head out._

" _I will." Yami said as he was heading out the door._

 _Just when Yami came out, Yugi walked back over to Yami._

" _What was that all about, Yami?" Yugi said as he held his hand out for Yami to take._

 _Yami then began to hold Yugi's hand._

" _Well, um…" Yami began to say, a little hesitant._

" _What is it?" Yugi asked, curiously._

" _Your grandpa said that he needs to tell you something very important when we get home today." Yami said as he and Yugi were now walking away from the game shop._

 _As they were both walking to Domino High, a question slipped into Yugi's mind…_

' _What does Grandpa have to tell me that's so important?'_

 **(Whoa! This chapter was quite nice and surprising, wasn't it? Do you think that Tea will apologize to Yugi and Yami? Please tell me in your reviews and I hope that you stay tuned for chapter three.)**


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